firstly, if segments are in BAD state (indicating that ideal state and external view status is mismatch in zk browser), then that can explain why you dont see some records in Pinot table even though they are in the topic. If segment is OFFLINE/ERROR state, it will not be queried. Restarting the servers or resetting the segments should help. Exceptions will be thrown in server logs, if any issues during restrat/reset.
secondly, if the topic for an existing realtime Pinot table was deleted, and then recreated, then it is possible that the table goes into a bad state. If you delete topic, the offsets all change. Pinot maintains its own offsets checkpointing in zookeeper.